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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ), 'gf_id' => 'ORTHO05D001127', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ), 'data_identifier' => 'ORTHO05D001127', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001127', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '479', 'num_species' => '70' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'AagrBONN_evm.TU.Sc2ySwM_228.2203' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2210' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2215' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2216' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.410' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2185' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4043' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1415' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1416' => 'aag', 'Actinidia15580' => 'ach', 'Actinidia18604' => 'ach', 'Actinidia18620' => 'ach', 'Actinidia18622' => 'ach', 'Actinidia34729' => 'ach', 'Actinidia36454' => 'ach', 'Aqoxy2G01086' => 'aox', 'Aqoxy2G01087' => 'aox', 'Aqoxy2G01088' => 'aox', 'Aqoxy2G01090' => 'aox', 'Aqoxy2G01091' => 'aox', 'Aqoxy4G02736' => 'aox', 'Aqoxy4G02737' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1HQW99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1U41EY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5RBN9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N5SM8A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VG9JMI' => 'arhy', 'ATR0090G004' => 'atr', 'ATR0090G007' => 'atr', 'ATR0090G025' => 'atr', 'ATR0090G026' => 'atr', 'ATR0090G033' => 'atr', 'ATR0090G043' => 'atr', 'ATR0145G001' => 'atr', 'ATR0210G028' => 'atr', 'ATR0665G123' => 'atr', 'ATR0820G032' => 'atr', 'ATR0820G175' => 'atr', 'ATR0820G279' => 'atr', 'Atru.chr3.3194' => 'acertr', 'Atru.chr3.3196' => 'acertr', 'Atru.chr3.3198' => 'acertr', 'Atru.chr3.3199' => 'acertr', 'Atru.chr3.3202' => 'acertr', 'Atru.chr3.3203' => 'acertr', 'Atru.chr3.3253' => 'acertr', 'Atru.chr3.3254' => 'acertr', 'CAN.G143.4' => 'can', 'CAN.G143.5' => 'can', 'CAN.G745.1' => 'can', 'CAN.G745.2' => 'can', 'CANSAT25G0836' => 'cansat', 'CANSAT25G1561' => 'cansat', 'CANSAT54G1266' => 'cansat', 'CANSAT54G1362' => 'cansat', 'CANSAT54G1664' => 'cansat', 'Ca_01652_v3' => 'car', 'Ca_19416_v3' => 'car', 'Cc01_g08920' => 'ccan', 'Cc01_g08940' => 'ccan', 'Cfa009999' => 'cfa', 'Cfa010000' => 'cfa', 'Cfa010001' => 'cfa', 'Cfa021373' => 'cfa', 'Ciclev10018035m.g' => 'ccl', 'Ciclev10023532m.g' => 'ccl', 'Ciclev10029937m.g' => 'ccl', 'Ciclev10030149m.g' => 'ccl', 'CiPaw.01G259400' => 'cil', 'CiPaw.09G213200' => 'cil', 'CiPaw.13G134500' => 'cil', 'CiPaw.14G033900' => 'cil', 'CiPaw.14G098900' => 'cil', 'ClCG01G012130' => 'cla', 'COL.COLO4_09592' => 'col', 'COL.COLO4_34024' => 'col', 'COL.COLO4_34025' => 'col', 'Cpa.g.sc195.11' => 'cpa', 'Cpa.g.sc54.8' => 'cpa', 'CsaV3_1G014960' => 'csa', 'CsaV3_1G015880' => 'csa', 'CSS0013363' => 'camsi', 'CSS0021844' => 'camsi', 'CSS0025316' => 'camsi', 'CSS0035816' => 'camsi', 'CSS0036059' => 'camsi', 'CSS0036733' => 'camsi', 'CSS0045774' => 'camsi', 'CSS0049116' => 'camsi', 'DCAR_001837' => 'dca', 'DCAR_001838' => 'dca', 'DCAR_012206' => 'dca', 'DCAR_012207' => 'dca', 'DCAR_029274' => 'dca', 'DCAR_029275' => 'dca', 'Dinv12844' => 'din', 'Dinv12847' => 'din', 'Dinv12851' => 'din', 'Dinv22826' => 'din', 'Dinv22827' => 'din', 'Dinv22829' => 'din', 'Dinv22830' => 'din', 'Dinv22831' => 'din', 'Dinv42537' => 'din', 'Duzib093G1253' => 'dzi', 'Duzib170G0289' => 'dzi', 'Duzib170G0976' => 'dzi', 'ECA233G0158' => 'eca', 'ECA236G0762' => 'eca', 'ECA236G1953' => 'eca', 'ECA236G2074' => 'eca', 'ECA236G3789' => 'eca', 'ECA236G3946' => 'eca', 'ECA238G2967' => 'eca', 'Eucgr.E00351' => 'egr', 'Eucgr.G02686' => 'egr', 'Eucgr.G02687' => 'egr', 'Eucgr.G02688' => 'egr', 'Eucgr.H04819' => 'egr', 'Eucgr.H04820' => 'egr', 'FAN01G0091' => 'fan', 'FAN01G1461' => 'fan', 'FAN03G0574' => 'fan', 'FAN03G0893' => 'fan', 'FAN03G2008' => 'fan', 'FAN06G1722' => 'fan', 'FAN06G2685' => 'fan', 'FAN06G4307' => 'fan', 'FAN06G4659' => 'fan', 'FAN10G1659' => 'fan', 'FAN11G0149' => 'fan', 'FAN11G0736' => 'fan', 'FAN11G1718' => 'fan', 'FAN11G1935' => 'fan', 'FAN11G2411' => 'fan', 'FAN11G2837' => 'fan', 'FAN11G3294' => 'fan', 'FAN16G0132' => 'fan', 'FAN16G1302' => 'fan', 'FAN21G4052' => 'fan', 'FAN25G3088' => 'fan', 'FvH4_3g08590' => 'fve', 'FvH4_3g08600' => 'fve', 'FvH4_3g25280' => 'fve', 'FvH4_3g25310' => 'fve', 'FvH4_3g25320' => 'fve', 'FvH4_3g25340' => 'fve', 'FvH4_7g08370' => 'fve', 'FvH4_7g08383' => 'fve', 'FvH4_7g08390' => 'fve', 'Glyma.02G044500' => 'gma', 'Glyma.12G090800' => 'gma', 'Glyma.12G090900' => 'gma', 'Glyma.12G092400' => 'gma', 'Glyma.12G185800' => 'gma', 'Glyma.20G119800' => 'gma', 'Gohir.A01G076000' => 'ghi', 'Gohir.A01G076100' => 'ghi', 'Gohir.A04G068828' => 'ghi', 'Gohir.A04G106000' => 'ghi', 'Gohir.A04G106033' => 'ghi', 'Gohir.D01G063400' => 'ghi', 'Gohir.D01G063600' => 'ghi', 'Gohir.D01G064950' => 'ghi', 'Gohir.D04G098266' => 'ghi', 'Gohir.D04G145800' => 'ghi', 'Gohir.D04G146000' => 'ghi', 'Gohir.D05G082650' => 'ghi', 'Gorai.002G084000' => 'gra', 'Gorai.002G084100' => 'gra', 'Gorai.002G085800' => 'gra', 'Gorai.002G086400' => 'gra', 'Gorai.009G084300' => 'gra', 'Gorai.009G400600' => 'gra', 'Gorai.012G131900' => 'gra', 'Gorai.012G132000' => 'gra', 'GSVIVG01036097001' => 'vvi', 'GSVIVG01036098001' => 'vvi', 'HanXRQChr04g0123611' => 'han', 'HanXRQChr05g0147741' => 'han', 'HanXRQChr05g0147761' => 'han', 'HanXRQChr06g0168781' => 'han', 'HanXRQChr06g0168791' => 'han', 'HanXRQChr06g0168801' => 'han', 'HanXRQChr07g0194061' => 'han', 'HanXRQChr08g0217301' => 'han', 'HanXRQChr13g0397191' => 'han', 'Haze_16730' => 'cav', 'Hma1.2p1_0478F.1_g161240' => 'hma', 'Hma1.2p1_0587F.1_g184150' => 'hma', 'Hma1.2p1_0587F.1_g184160' => 'hma', 'Hma1.2p1_0756F.1_g213220' => 'hma', 'Hma1.2p1_0898F.1_g234400' => 'hma', 'Hma1.2p1_1491F.1_g286700' => 'hma', 'HPP92_017298' => 'vpl', 'HPP92_017299' => 'vpl', 'HPP92_017300' => 'vpl', 'Lj1A234T41' => 'lonja', 'Lj1A234T43' => 'lonja', 'Lj1A235T67' => 'lonja', 'Lj1A235T68' => 'lonja', 'Lj1A255T70' => 'lonja', 'Lj1A255T71' => 'lonja', 'Lj1A255T72' => 'lonja', 'Lj1A256T62' => 'lonja', 'Lj1A256T64' => 'lonja', 'Lj1C234T14' => 'lonja', 'Lj1C234T5' => 'lonja', 'Lj1C234T6' => 'lonja', 'Lj1C235G7' => 'lonja', 'Lj1C256G0' => 'lonja', 'Lj1C256T9' => 'lonja', 'Lj1P235T17' => 'lonja', 'Lj1P255T54' => 'lonja', 'Lj2C967T10' => 'lonja', 'Lj2C967T9' => 'lonja', 'Lj3C925T10' => 'lonja', 'Lj3C925T8' => 'lonja', 'Lj3C925T9' => 'lonja', 'Lj3g0001807' => 'lja', 'Lj3g0004749' => 'lja', 'Lj3g0025293' => 'lja', 'Lj4C536G0' => 'lonja', 'Lsat_1_v5_gn_0_8200' => 'lsa', 'Lsat_1_v5_gn_0_8220' => 'lsa', 'Lsat_1_v5_gn_2_104141' => 'lsa', 'Lsat_1_v5_gn_6_39141' => 'lsa', 'Lsat_1_v5_gn_7_11281' => 'lsa', 'Lsat_1_v5_gn_7_11300' => 'lsa', 'Lsat_1_v5_gn_9_67381' => 'lsa', 'Manes.01G089300' => 'mes', 'Manes.01G089400' => 'mes', 'Manes.01G089500' => 'mes', 'Manes.02G045600' => 'mes', 'Manes.04G002300' => 'mes', 'Manes.04G002400' => 'mes', 'Mapoly0008s0175' => 'mpo', 'Mapoly0010s0025' => 'mpo', 'Mapoly0010s0105' => 'mpo', 'Mapoly0010s0106' => 'mpo', 'Mapoly0010s0107' => 'mpo', 'Mapoly0010s0108' => 'mpo', 'Mapoly0010s0110' => 'mpo', 'Mapoly0010s0111' => 'mpo', 'Mapoly0010s0112' => 'mpo', 'Mapoly0010s0115' => 'mpo', 'Mapoly0010s0116' => 'mpo', 'Mapoly0010s0117' => 'mpo', 'Mapoly0021s0001' => 'mpo', 'Mapoly0024s0044' => 'mpo', 'Mapoly0026s0053' => 'mpo', 'Mapoly0028s0004' => 'mpo', 'Mapoly0031s0195' => 'mpo', 'Mapoly0032s0076' => 'mpo', 'Mapoly0032s0077' => 'mpo', 'Mapoly0040s0045' => 'mpo', 'Mapoly0045s0001' => 'mpo', 'Mapoly0045s0002' => 'mpo', 'Mapoly0050s0040' => 'mpo', 'Mapoly0050s0041' => 'mpo', 'Mapoly0082s0058' => 'mpo', 'Mapoly0085s0057' => 'mpo', 'Mapoly0085s0058' => 'mpo', 'Mapoly0085s0059' => 'mpo', 'Mapoly0085s0060' => 'mpo', 'Mapoly0108s0024' => 'mpo', 'Mapoly0112s0025' => 'mpo', 'Mapoly0130s0001' => 'mpo', 'Mapoly0170s0016' => 'mpo', 'Mapoly0180s0001' => 'mpo', 'Mapoly0180s0002' => 'mpo', 'Mapoly0180s0003' => 'mpo', 'Mapoly0180s0028' => 'mpo', 'Mapoly0180s0029' => 'mpo', 'Mapoly0193s0003' => 'mpo', 'Mapoly0193s0005' => 'mpo', 'Mapoly0193s0007' => 'mpo', 'Mapoly0193s0008' => 'mpo', 'Mapoly0193s0009' => 'mpo', 'Mapoly0193s0010' => 'mpo', 'Mapoly0193s0011' => 'mpo', 'Mapoly0193s0018' => 'mpo', 'Mapoly0193s0019' => 'mpo', 'Mapoly0193s0020' => 'mpo', 'Mapoly0193s0021' => 'mpo', 'Mapoly0197s0001' => 'mpo', 'Mapoly0197s0002' => 'mpo', 'Mapoly0210s0002' => 'mpo', 'Mapoly0210s0003' => 'mpo', 'Mapoly0242s0002' => 'mpo', 'Mapoly0242s0003' => 'mpo', 'Mapoly0352s0001' => 'mpo', 'Mapoly0352s0002' => 'mpo', 'Mapoly0352s0003' => 'mpo', 'Mapoly0930s0001' => 'mpo', 'Mapoly1268s0001' => 'mpo', 'Mapoly1685s0001' => 'mpo', 'Mapoly1984s0001' => 'mpo', 'Mapoly2349s0001' => 'mpo', 'MBI01_g40632_MAGBIO' => 'mbi', 'MBI14_g08992_MAGBIO' => 'mbi', 'MBI17_g29784_MAGBIO' => 'mbi', 'MBI17_g29786_MAGBIO' => 'mbi', 'MBI17_g29791_MAGBIO' => 'mbi', 'MBI17_g29793_MAGBIO' => 'mbi', 'MBI17_g29794_MAGBIO' => 'mbi', 'MD03G1148000' => 'mdo', 'MD07G1084100' => 'mdo', 'MD11G1166900' => 'mdo', 'MD11G1167000' => 'mdo', 'MD11G1167100' => 'mdo', 'MD11G1167300' => 'mdo', 'MD11G1167400' => 'mdo', 'MD11G1169200' => 'mdo', 'MD11G1169300' => 'mdo', 'Medtr2g086620' => 'mtr', 'Medtr2g086630' => 'mtr', 'Medtr2g086640' => 'mtr', 'Medtr4g052770' => 'mtr', 'Medtr4g052780' => 'mtr', 'MELO3C004688.2' => 'cme', 'Migut.N02480' => 'egut', 'Migut.N02481' => 'egut', 'Migut.N02482' => 'egut', 'Nitab4.5_0000227g0110' => 'nta', 'Nitab4.5_0000691g0090' => 'nta', 'Nitab4.5_0002603g0040' => 'nta', 'Nitab4.5_0002914g0130' => 'nta', 'Nitab4.5_0003927g0040' => 'nta', 'Nitab4.5_0006120g0010' => 'nta', 'Nitab4.5_0006120g0060' => 'nta', 'Nitab4.5_0010781g0020' => 'nta', 'Nitab4.5_0010845g0020' => 'nta', 'Nitab4.5_0013750g0010' => 'nta', 'Nitab4.5_0015960g0010' => 'nta', 'Nitab4.5_0015960g0020' => 'nta', 'Oeu002367.1' => 'oeu', 'Oeu002369.1' => 'oeu', 'Oeu026611.1' => 'oeu', 'Oeu026612.1' => 'oeu', 'Oeu027158.1' => 'oeu', 'Os09g0568500' => 'osa', 'Os09g0568600' => 'osa', 'Os09g0568700' => 'osa', 'Peaxi162Scf00040g00024' => 'pax', 'Peaxi162Scf00040g10021' => 'pax', 'Peaxi162Scf00040g10023' => 'pax', 'Peaxi162Scf00195g00104' => 'pax', 'Peaxi162Scf00609g00052' => 'pax', 'Peaxi162Scf00725g00021' => 'pax', 'Peaxi162Scf00725g00023' => 'pax', 'Peaxi162Scf00725g00024' => 'pax', 'PGR102G0354' => 'pgr', 'PGR142G2318' => 'pgr', 'PGSC0003DMG400001279' => 'stu', 'PGSC0003DMG400001280' => 'stu', 'PGSC0003DMG400026333' => 'stu', 'PGSC0003DMG400026352' => 'stu', 'PGSC0003DMG400026353' => 'stu', 'PGSC0003DMG400031901' => 'stu', 'PGSC0003DMG400041571' => 'stu', 'Phvul.005G122900' => 'pvu', 'Potri.004G194600' => 'ptr', 'Potri.008G016700' => 'ptr', 'Potri.008G084300' => 'ptr', 'Potri.009G157100' => 'ptr', 'Potri.010G240500' => 'ptr', 'Potri.010G240600' => 'ptr', 'Potri.010G240700' => 'ptr', 'Potri.013G116500' => 'ptr', 'Pp3c11_1150' => 'ppa', 'Pp3c15_18180' => 'ppa', 'Pp3c23_14870' => 'ppa', 'Pp3c7_25050' => 'ppa', 'Pp3c7_25080' => 'ppa', 'Prupe.2G051900' => 'ppe', 'Prupe.2G052000' => 'ppe', 'Prupe.2G110800' => 'ppe', 'Prupe.2G111000' => 'ppe', 'Prupe.2G111100' => 'ppe', 'Prupe.6G132900' => 'ppe', 'Prupe.6G133000' => 'ppe', 'Prupe.6G133100' => 'ppe', 'Prupe.6G133200' => 'ppe', 'Prupe.6G133300' => 'ppe', 'Prupe.6G133400' => 'ppe', 'Psat5g257520' => 'psa', 'Psat5g257560' => 'psa', 'Psat5g258200' => 'psa', 'Psat7g187480' => 'psa', 'PSO339G1152' => 'pso', 'PSO339G5841' => 'pso', 'PSO339G6274' => 'pso', 'PSO384G0116' => 'pso', 'PSO801G0627' => 'pso', 'PSO801G0714' => 'pso', 'QL01p010020' => 'qlo', 'QL01p010029' => 'qlo', 'QL01p011965' => 'qlo', 'QL01p012046' => 'qlo', 'QL01p012048' => 'qlo', 'QL04p046831' => 'qlo', 'RcHm_v2.0_Chr1g0340191' => 'rch', 'RcHm_v2.0_Chr1g0340211' => 'rch', 'RcHm_v2.0_Chr1g0340251' => 'rch', 'RcHm_v2.0_Chr5g0046741' => 'rch', 'RcHm_v2.0_Chr5g0046751' => 'rch', 'RcHm_v2.0_Chr5g0046771' => 'rch', 'RcHm_v2.0_Chr5g0046781' => 'rch', 'RcHm_v2.0_Chr5g0046791' => 'rch', 'RcHm_v2.0_Chr5g0046801' => 'rch', 'RcHm_v2.0_Chr5g0046811' => 'rch', 'RcHm_v2.0_Chr5g0046821' => 'rch', 'Sabra04G0132300' => 'sbr', 'SalBow3G0487' => 'sbo', 'SalBow3G1261' => 'sbo', 'SalBow6G0783' => 'sbo', 'Sed0021001' => 'sed', 'SEGI_00342' => 'sgi', 'SEGI_12011' => 'sgi', 'SEGI_14790' => 'sgi', 'SEGI_27296' => 'sgi', 'SEGI_32096' => 'sgi', 'SMO203G0087' => 'smo', 'SMO203G0139' => 'smo', 'Solyc11g006730.1' => 'sly', 'Solyc11g068570.1' => 'sly', 'Solyc11g068580.1' => 'sly', 'Solyc11g068590.1' => 'sly', 'Solyc11g068600.1' => 'sly', 'Sopen11g002660' => 'spe', 'Sopen11g027290' => 'spe', 'Sopen11g027300' => 'spe', 'Sopen11g027310' => 'spe', 'Sopen11g027320' => 'spe', 'TAR248G0002' => 'tar', 'TAR369G0015' => 'tar', 'TAR369G0115' => 'tar', 'TAR369G0179' => 'tar', 'TAR369G0370' => 'tar', 'TAR369G0495' => 'tar', 'TAR369G0711' => 'tar', 'TAR369G0759' => 'tar', 'TAR369G0846' => 'tar', 'TAR369G0900' => 'tar', 'TAR369G0927' => 'tar', 'TAR369G1013' => 'tar', 'TAR369G1094' => 'tar', 'TAR374G1022' => 'tar', 'TAR623G0685' => 'tar', 'TAR624G0328' => 'tar', 'TAR624G1154' => 'tar', 'TAR633G0190' => 'tar', 'TAR633G2050' => 'tar', 'TAR636G0044' => 'tar', 'TAR636G1464' => 'tar', 'TAR636G3393' => 'tar', 'Thecc.07G046600' => 'tca', 'Thecc.09G192600' => 'tca', 'Thecc.09G192700' => 'tca', 'Thecc.09G280500' => 'tca', 'Thecc.09G280600' => 'tca', 'Thecc.09G280700' => 'tca', 'TPR.G23842' => 'tpr', 'TPR.G368' => 'tpr', 'TPR.G4491' => 'tpr', 'TPR.G4511' => 'tpr', 'TPR.G4589' => 'tpr', 'TWI31G0867' => 'twi', 'TWI31G1213' => 'twi', 'TWI34G0139' => 'twi', 'TWI34G1061' => 'twi', 'TWI34G1079' => 'twi', 'TWI34G1598' => 'twi', 'TWI75G1264' => 'twi', 'TWI79G0674' => 'twi', 'TWI79G1669' => 'twi', 'VMungo1080G0489' => 'vmu', 'Zm00001eb095950' => 'zma' ) $gf_id = 'ORTHO05D001127' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001127' ) $data_identifier = 'ORTHO05D001127' $data_type = 'gf_id' $species_gene_counts = array( 'aag' => (int) 9, 'ach' => (int) 6, 'aox' => (int) 7, 'arhy' => (int) 5, 'atr' => (int) 12, 'acertr' => (int) 8, 'can' => (int) 4, 'cansat' => (int) 5, 'car' => (int) 2, 'ccan' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 3, 'eca' => (int) 7, 'egr' => (int) 6, 'fan' => (int) 21, 'fve' => (int) 9, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 8, 'vvi' => (int) 2, 'han' => (int) 9, 'cav' => (int) 1, 'hma' => (int) 6, 'vpl' => (int) 3, 'lonja' => (int) 23, 'lja' => (int) 3, 'lsa' => (int) 7, 'mes' => (int) 6, 'mpo' => (int) 63, 'mbi' => (int) 7, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 3, 'nta' => (int) 12, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 7, 'pvu' => (int) 1, 'ptr' => (int) 8, 'ppa' => (int) 5, 'ppe' => (int) 11, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 11, 'sbr' => (int) 1, 'sbo' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'tar' => (int) 22, 'tca' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 9, 'vmu' => (int) 1, 'zma' => (int) 1 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb095950' $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